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Atroshchenko M, Dementieva N, Shcherbakov Y, Nikolaeva O, Azovtseva A, Ryabova A, Nikitkina E, Makhmutova O, Datsyshin A, Zakharov V, Zaitsev A. The Genetic Diversity of Horse Native Breeds in Russia. Genes (Basel) 2023; 14:2148. [PMID: 38136970 PMCID: PMC10743158 DOI: 10.3390/genes14122148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k ® array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.
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Affiliation(s)
- Mikhail Atroshchenko
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Natalia Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Yuri Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Olga Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Anastasiia Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Anna Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Elena Nikitkina
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia; (Y.S.); (O.N.); (A.A.); (A.R.); (E.N.)
| | - Oksana Makhmutova
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Andrey Datsyshin
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Viktor Zakharov
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
| | - Alexander Zaitsev
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia; (M.A.); (O.M.); (A.D.); (V.Z.); (A.Z.)
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Choudhury MP, Wang Z, Zhu M, Teng S, Yan J, Cao S, Yi G, Liu Y, Liao Y, Tang Z. Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses. Genes (Basel) 2023; 14:1934. [PMID: 37895283 PMCID: PMC10606273 DOI: 10.3390/genes14101934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.
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Affiliation(s)
- Md. Panir Choudhury
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Bangladesh Livestock Research Institute, Ministry of Fisheries and Livestock, Savar, Dhaka 1341, Bangladesh
| | - Zihao Wang
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Min Zhu
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Shaohua Teng
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Jing Yan
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Shuwei Cao
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Guoqiang Yi
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Nanning 530001, China
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A. The Genetic Diversity of Stallions of Different Breeds in Russia. Genes (Basel) 2023; 14:1511. [PMID: 37510415 PMCID: PMC10378902 DOI: 10.3390/genes14071511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heterozygous and homozygous ROH regions, evaluated inbreeding using FROH analysis, and generated a population structure using Admixture 1.3 software. Our findings indicate that the Arabian breed is an ancestor of many horse breeds. The study of the full-genome architectonics of breeds is of great practical importance for preserving the genetic characteristics of breeds and managing breeding. Studies were carried out to determine homozygous regions in individual breeds and search for candidate genes in these regions. Fifty-six candidate genes for the influence of selection pressure were identified. Our research reveals genetic diversity consistent with breeding directions and the breeds' history of origin.
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Affiliation(s)
- Natalia Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg 196625, Russia
| | - Elena Nikitkina
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg 196625, Russia
| | - Yuri Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg 196625, Russia
| | - Olga Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg 196625, Russia
| | - Olga Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg 196625, Russia
| | - Anna Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg 196625, Russia
| | - Mikhail Atroshchenko
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Divovo, Rybnovskij District 391105, Russia
| | - Oksana Makhmutova
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Divovo, Rybnovskij District 391105, Russia
| | - Alexander Zaitsev
- All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Divovo, Rybnovskij District 391105, Russia
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